Microalgal species of the genus Nannochloropsis have attracted considerable interest for various commercial applications. For example, several Nannochloropsis species are commonly cultivated in fish hatcheries as a food source for zooplankton production, such as rotifers and copepods, which in turn is used as feed for rearing larvae of many species of mollusks, crustaceans, and fish. Further, several Nannochloropsis species are well known as being capable to build up a high concentration of a range of different valuable pigments such as astaxanthin, canthaxanthin, chlorophyll a, and zeaxanthin. Additionally, many Nannochloropsis species are considered as promising microorganisms for industrial applications because of their ability to accumulate high levels of polyunsaturated fatty acids (PUFA), especially eicosapentaenoic acid (EPA). As a result, Nannochloropsis is often recognized as being potentially a good source for the dietary supplement of omega-3 fatty acids and other important PUFAs for human consumption for prevention of several diseases and medical conditions.
Moreover, Nannochloropsis has been increasingly considered to have good potentials as a bioreactor to carry or produce valuable heterologous protein because of the low production cost, high expression level, relatively simple culture conditions. More recently, Nannochloropsis has gained commercial importance as being potentially suitable for algal biofuel production, and thus has attracted considerable attention due to its relative ease of growth and high oil content (see, e.g., Radakovits et al., Eukaryotic Cells, 486-501, Vol. 9, No. 4, 2010). Nevertheless, optimization of culture conditions for selected Nannochloropsis species has been reported to be potentially a challenge, because the fatty acid content of individual species and isolates can vary considerably under different environmental conditions in the field and in laboratory culture. For example, cellular lipid content of some marine Nannochloropsis species has been reported to be highly affected by the availability of nitrogen sources in the growth medium. Also, the production of fatty acids in Nannochloropsis is often directly dependent on CO2 concentration in aerated suspension cultures. Another potential challenge for the use of Nannochloropsis in industrial applications is that the accumulation of fatty acids including PUFA in Nannochloropsis, for example Nannochloropsis limnetica, has been reported to be highly dependent on growth phases; i.e. higher PUFA cellular content in the stationary phase of growth and even considerably higher in non-aerated cultures.
Therefore, there exists a continuing need to develop novel strains of Nannochloropsis that are more stable in different growth environments and thus more suitable to industrial production. When transgenic approaches are considered, there is an additional need in the art to develop new and useful tools and methods for the transformation of Nannochloropsis microorganisms, which in turn will facilitate the generation of novel strains with enhanced commercial value. Finally, there also exists an ongoing need to develop materials and methods for mutation or inactivation of specific genes by homologous recombination in Nannochloropsis microorganisms, providing a new way to alter cellular metabolism and to study the function of specific genes and biosynthetic pathways in Nannochloropsis. 
The present application discloses materials and methods that may find uses in, for example, genetic engineering of cells and organisms. Particularly, the materials and methods disclosed herein can be used to confer the tolerance of recombinant cells to chemical inhibitors that inhibit acetohydroxyacid synthase activity such as, for example, herbicide compounds and therefore can be useful in, for example, controlling unwanted contaminant organisms that are sensitive to such herbicides.